Spectral and structural features of bio-composite films of graphene oxide and molybdenum disulphide with molecules of 5-bromouracyl and 5-bromo-2’-deoxyuridine

  • Yu. V. Rubin B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, 47 Nauky Avenue, Kharkiv, 61103, Ukraine
  • A. Yu. Ivanov B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, 47 Nauky Avenue, Kharkiv, 61103, Ukraine https://orcid.org/0000-0002-2975-3052
  • L. F. Belous B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, 47 Nauky Avenue, Kharkiv, 61103, Ukraine
  • V. A. Karachevtsev B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, 47 Nauky Avenue, Kharkiv, 61103, Ukraine https://orcid.org/0000-0003-4580-6465
Keywords: DNA bases, nucleosides, graphene, graphene oxide, molybdenum disulfide, quantum mechanical calculations, infrared Fourier-transform spectroscopy


Background: Recently, composite materials based on nanoparticles and biological molecules have been intensively studied due to the unique physicochemical and biophysical properties and prospects of application in various fields of technology, engineering and medicine. Many laboratories conduct experiments with composite materials based on carbon nanoparticles and various 2D nanomaterials in order to create sensitive biosensors based on them, to develop new functional materials for biology and medicine. A wide range of practical applications requires fundamental knowledge about the structure of the created composites, the interaction energy between the components and their spectral characteristics.

Objectives: The purpose of the work was to study the structural features of biocomposite films of graphene oxide (GO) and molybdenum disulfide MoS2 with 5-bromouracil (5BrU) and 5-bromo-2'-deoxyuridine (5BrdU) and to obtain information on the interaction between their components based on data from the infrared Fourier spectroscopy and quantum chemical calculations.

Materials and methods: For the measurements, a vacuum infrared Fourier spectrometer was used. The composite films were created by the drop casting method based on graphene oxide from GRAPHENEA, an aqueous suspension of MoS2 molybdenum disulfide powder, as well as 5BrU and 5BrdU biomolecules. For the quantum-chemical calculations of model structures the Gaussian 09 and the Firefly 8.0 programs were used. In last one the GAMESS (USA) program code was partially used.

Results: The frequencies and intensities of infrared absorption bands of the biocomposite films (5BrU/GO, 5BrU/MoS2, 5BrdU/GO and 5BrdU/MoS2) with different numbers of biomolecules were obtained. The absorption bands of composite films are assigned to the corresponding types of normal vibrations. The interaction energies in model structures are determined. The amorphous (disordered) structure of 5BrU clusters in 5BrU/GO composites at a low concentration of biomolecules has been established. It is shown that the MoS2 composites are more heterogeneous than the GO composites.

Conclusions: The absorption band of CO vibrations with a frequency of 1783 cm–1 as well as the bands of the out-of-plane deformation vibrations γNH of 5BrU are sensitive to the structure of 5BrU clusters in composite films. It has been demonstrated that graphene oxide in the composite films affects the conformational equilibrium of 5BrdU. It has been established that structures with stacking between the pyrimidine ring of a nucleoside and the basal plane of graphene oxide are the most energetically favorable.


Download data is not yet available.


Yin PT, Shah S, Chhowalla M, Lee K-B. Design, synthesis, and characterization of graphene−nanoparticle hybrid materials for bioapplications. Chem. Rev. 2015;115(7):2483–532. http://doi.org/10.1021/cr500537t

Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. Nature Nanotechnology. 2016;11: 127–36. https://doi.org/10.1038/nnano.2015.307

Xiao L, Xu L, Gao Ch, Zhang Yu, Yao Q, Zhang G-J. A MoS2 nanosheet-based fluorescence biosensor for simple and quantitative analysis of DNA methylation. Sensors. 2016;16:1561–71. https://doi.org/10.3390/s16101561

Yadav V, Roy S, Singh P, Khan Z, Jaiswal A. 2D MoS2-based nanomaterials for therapeutic, bioimaging, and biosensing applications. Small. 2019;15:1803706–39. https://doi.org/10.1002/smll.201803706

Saenger W. Principles of Nucleic Acids Structure. Springer-Verlag: New York; 1984. 556 p. https://doi.org/10.1016/0307-4412(85)90046-9

Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM. On the mechanism of the mutagenic action of 5-bromouracil: a DFT study of uracil and 5-bromouracil in a water cluster. J. Phys. Chem. A, 2009;113:2233–35. https://doi.org/10.1021/jp811007j

Abdoul-Carime H, Huels MA, Illenberger E, and Sanche L. Sensitizing DNA to secondary electron damage: resonant formation of oxidative radicals from 5-halouracils. J. Am. Chem. Soc. 2001;123:5354–55. https://doi.org/10.1021/ja003952d

Hashiya F, Saha A, Kizaki S, Li Y, Sugiyama H. Locating the uracil-5-yl radical formed upon photoirradiation of 5-bromouracil-substituted DNA. Nucleic Acids Research, 2014;42(22):13469–73. https://doi.org/ 10.1093/nar/gku1133

Ivanov AYu, Leontiev VS, Belous LF, Rubin YuV, Karachevtsev VA. Infrared spectra of 5-fluorouracil molecules isolated in inert Ar matrices, and their films on graphene oxide at 6K. Low Temperature Physics. 2017;43:400–8. https://doi.org/10.1063/1.4979957

Ivanov AYu, Plokhotnichenko AM, Karachevtsev VA. Enhancement of the absorption bands in the infrared spectra of low-temperature uracil films by interference. Low Temperature Physics. 2018;44(11):1215–18. https://doi.org/10.1063/1.5062163

Ivanov AYu, Rubin YuV, Belous LF, Karachevtsev VA. Structures and infrared spectra of 5-chlorouracil molecules in the low-temperature inert Ar, Ne matrices and composite films with oxide graphene. Low Temperature Physics. 2018;44(8):847–55. https://doi.org/10.1063/1.5049170

Ivanov AYu, Plokhotnichenko AM, Radchenko ED, Sheina GG, Blagoi YuP. FTIR spectroscopy of uracil derivatives isolated in Kr, Ar and Ne matrices: matrix effect and Fermi resonance. J. Mol. Struct. 1995;372:91–100. https://doi.org/10.1016/0022-2860(95)08976-4

Ivanov AYu, Krasnokutski SA, Sheina GG. Molecular structures of thymidine isomers isolated in low-temperature inert matrices. Low Temp. Phys. 2003;29:809–14. https://doi.org/10.1063/1.1614199

Ivanov AYu, Karachevtsev VA. FTIR spectra and conformations of 2′-deoxyuridine in Kr matrices. Low Temp. Phys. 2007;33:590–5. https://doi.org/10.1063/1.2755193

Ivanov AYu, Plokhotnichenko AM. A low-temperature quartz microbalance. Instr. Experim. Techn. 2009;52:308–11. https://doi.org/10.1134/S0020441209020341

Wojdyr M. Fityk: a general purpose peak fitting program. J. Appl. Cryst. 2010;43:1126–8. https://doi.org/10.1107/S0021889810030499

Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 16, Revision B.01, Gaussian, Inc., Wallingford CT, 2016.

Granovsky Alex A. Firefly Version 7.1.G [Internet]. 2009 [cited 2020 May 29]. Available from: http://classic.chem.msu.su/gran/firefly/index.html

Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, et al. General atomic and molecular electronic structure system. J. Comput. Chem. 1993;14:1347–63. https://doi.org/10.1002/jcc.540141112

Grimme S, Ehrlich S, Goerigk L. Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 2011;32:1456–65. https://doi.org/10.1002/jcc.21759

Ivanov AYu, Rubin YuV, Egupov SA, Belous LF, Karachevtsev VA. Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil. Low Temp. Phys. 2013;39:546–56. https://doi.org/10.1063/1.4811260

Ivanov AYu, Stepanian SG, Karachevtsev VA. Adamowicz L. Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations. Low Temp. Phys. 2019;45:1008–18. https://doi.org/10.1063/1.5121271

Rozenberg M, Shoham G, Reva I, Fausto R. Low temperature Fourier transform infrared spectra and hydrogen bonding in polycrystalline uracil and thymine. Spectrochimica Acta Part A, 2004;60:2323–36. https://doi.org/10.1016/j.saa.2003.12.006

Holroyd LF, van Mourik T. Stacking of the mutagenic base analogue 5-bromouracil: energy landscapes of pyrimidine dimers in gas phase and water. Phys. Chem. Chem. Phys. 2015;17:30364–70. https://doi.org/10.1039/C5CP04612B

Deegan RD, Bakajin O, Dupont TF, Huber G, Nagel SR, Witten TA. Capillary flow as the cause of ring stains from dried liquid drops. Nature. 1997;389:827–9. https://doi.org/10.1038/39827

Deegan RD, Bakajin O, Dupont TF, Huber G, Nagel SR, Witten TA. Contact line deposits in an evaporating drop. Phys. Rev. E. 2000;62:756–65. https://doi.org/10.1103/PhysRevE.62.756

Vovusha H, Sanyal B. Adsorption of nucleobases on 2D transition-metal dichalcogenides and graphene sheet: a first principles density functional theory study. RSC Adv. 2015;5:67427–34. https://doi.org/10.1039/C5RA14664J

Tsyganenko AA, Can F, Travert A, Maugé F. FTIR study of unsupported molybdenum sulfide — in situ synthesis and surface properties characterization. Applied Catalysis A: General. 2004;268:189–97. https://doi.org/10.1016/j.apcata.2004.03.038

How to Cite
Rubin, Y. V., Ivanov, A. Y., Belous, L. F., & Karachevtsev, V. A. (2020). Spectral and structural features of bio-composite films of graphene oxide and molybdenum disulphide with molecules of 5-bromouracyl and 5-bromo-2’-deoxyuridine. Biophysical Bulletin, (43), 71-84. https://doi.org/10.26565/2075-3810-2020-43-08
Biophysics of complex systems

Most read articles by the same author(s)